Card #5 in his record states: See personal papers* of Co. B Harris’s Batt’n from[?] Camp of Correction, Mobile, Ala.

* personal papers lined through

This referenced document might explain the reason for his imprisonment.

I am unable to locate Harris’ Battalion in Fold.3 nor in the NA Catalog of Military Service Records.

Nor could I find a record for Maj. R. A. Harris

…..

Here is some interesting material:

REDEEMED IN BLOOD is the story of the 57th Alabama Infantry Regiment, C.S.A. This late-war unit was mustered at Troy, in Pike County, Alabama, in March of 1863.

Composed primarily of old men and young boys, it was a unit filled to the brim with "reluctant rebels." Indeed, most had been conscripted into the Army against their will. The overwhelming majority were poor, but proud family men from the Wiregrass region of Pike, Butler, Barbour, Conecuh, Covington, Coffee, Dale, and Henry counties in Southeast Alabama.

Within the first year of field service, nearly one-third would choose to desert the Cause. However, of the two-thirds who did choose to stay and fight, they would soon redeem their unit's tainted reputation on the bloody battlefields of Resaca, Kennesaw Mountain, Peachtree Creek, Franklin, and Nashville. This is their story.
http://www.thebookpatch.com/BookStore/redeemed-in-blood-a-history-of-the-57th-alabama-infantry-regiment-csa/e6327254-62b0-4a9a-b127-5ac0d28b300c